[gmx-users] Correct use of gmx traj -mol ?

[Dallas Warren]

James,

Have you tried the following?  I interpret that to mean that the index
fill will contain a group like this:

[ Molecules ]
i1 i2 i3 i4 i5 i6 ….. in

Where each i term corresponds to a particular molecule within the
system, and that number i will match up with the residue numbers.  So
can either make that by hand, that there should be also a method via
make_ndx to output the residue numbers into a group too.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.



On Tue, 6 Nov 2018 at 12:12, James <james at ryley.com> wrote:
>
> Hi,
>
> I am interested in obtaining temperature readings that are corrected for
> velocity (meaning, if a molecule has a net velocity, that kinetic energy
> should not be counted as part of temperature). I suspect this is what the
> traj -mol option would do, but I can't get it to run without error.
>
> I am guessing the problem lies with my index files. The traj docs state
> that "When -mol is set, the numbers in the index file are interpreted as
> molecule numbers...". I don't understand this. All my index files contain
> are group headings and atom numbers. It seems like there would need to be
> another column that indicates molecule number (and I know such a column
> exists in some other file formats, but nothing I've read indicates that
> .ndx files can have extra columns).
>
> Any idea what I am doing wrong, or can anyone provide a set of test file on
> which "gmx traj -mol" can be successfully run?
>
> Sincerely,
> James
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